1. Slicer 101 IGT Edition Haiying Liu, M.S. Nobuhiko Hata, Ph.D.

2. © NIH National Center for Image-Guided Therapy, October 2006 Slide 2 Acknowledgements National Center for Image- Guided Therapy NIH 1U41RR019703 National Alliance for Medical Image Computing NIH U54EB005149

3. © NIH National Center for Image-Guided Therapy, October 2006 Slide 3 Outline of tutorial 1)Download and install Slicer-IGT 2)Learn Slicer basics 3)Obtain a plastic skull 4)Obtain a tracking device and setup the system 5)Connect Slicer to the tracking device 6)Register the tracking space to Slicer space 7)Perform navigation

4. © NIH National Center for Image-Guided Therapy, October 2006 Slide 4 Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.

5. © NIH National Center for Image-Guided Therapy, October 2006 Slide 5 Welcome to 3D Slicer IGT

6. © NIH National Center for Image-Guided Therapy, October 2006 Slide 6 What is 3D Slicer? 3D Slicer is… – An end-user application for 3D medical image computing research and Image Guided Therapy – A platform for research where new techniques can be plugged into a useful framework – A freely-downloadable program with source and binaries for Windows, Linux, Solaris and (increasingly) Mac OSX – NOT an FDA approved medical device and CANNOT be used clinically without proper research controls (IRB etc.) – NOT finished – some parts will work better than others and it is constantly evolving

7. © NIH National Center for Image-Guided Therapy, October 2006 Slide 7 Slicer background SPL Image Guided Surgery and Visualization (Kikinis, Westin, Hata, Halle, others) Slicer Application Pulled Together by Dave Gering 1997-1999 with VTK and Tcl Further Development and Architecture by Lauren O’Donnell 1999-2001 Ongoing Development of Slicer’s Base Primarily by Steve Pieper and Nicole Aucoin Many Modules and Contributions by Various Authors – BWH, MIT, MGH, Georgia Tech, UCSD, JHU... Now being used as a reference application platform for NA- MIC and NCITG

8. © NIH National Center for Image-Guided Therapy, October 2006 Slide 8 Features Load Medical Image Data: MR, CT in DICOM, GE, Analyze… XML-based File Format: MRML (Medical Reality Markup Language) Interactive Editor: Draw, Threshold, Math Morphology… Automated Segmenters: EM Segmentation, Fast Marching, Level Sets… Visualization: Model Building, Stereo Rendering, Animation… Registration: Manual, ITK… Measurement: Fiducial-Based, Volumetric, Polyhedral Intersection, Vessel Cross-Section, Osteotomy Planning IGT: Tracked Probes, Real-Time Images, Robot Control Additional Application-Specific Features in Modules…

9. © NIH National Center for Image-Guided Therapy, October 2006 Slide 9 Goal of tutorial Simulate the brain surgical navigation using a plastic skull and a tracking sensor

10. © NIH National Center for Image-Guided Therapy, October 2006 Slide 10 Download and install Slicer-IGT Slicer-IGT may be downloaded here: http://www.na-mic.org/Wiki/index.php/IGT-Tutorials Install the Slicer as follows: 1) The binary is for Windows XP. Be sure you have WinZip installed on your computer 2) Unzip the binary to any directory on your computer. A directory named “ slicer2.6-opt-win32-x86-2006-11-15 ” will be created. This is the top directory of the Slicer 3) Change to that directory using Windows Explorer 4) Create a shortcut for “ slicer2-win32-x86.exe ”

11. © NIH National Center for Image-Guided Therapy, October 2006 Slide 11 Learn the basics of Slicer Slicer-IGT may be run by double-clicking its shortcut on the desktop of your computer Sample data and tutorials of how to use 3D Slicer can be found at: http://wiki.na- mic.org/Wiki/index.php/Slicer:Workshops:User_Trainin g_101#Slicer_Training. Make sure you are confident to do the following: – Load volumes – Segment – Make models

12. © NIH National Center for Image-Guided Therapy, October 2006 Slide 12 Buy a plastic skull – Budget Life-size Skull ($29.95), Anatomical Chart Company (anatomical.com) Also available at – Lippincott Williams & Wilkins (lww.com) – Amazon.com and other international Amazon sites

13. © NIH National Center for Image-Guided Therapy, October 2006 Slide 13 Obtain a tracking system from NDI –Choose one of these tracking systems: Aurora, Polaris, or Polaris Vicra. Aurora is used to create this tutorial material. –Make sure you have a 6 DOF tracking sensor (The left picture is a copy from NDI website: http://www.ndigital.com/ aurora.php)

14. © NIH National Center for Image-Guided Therapy, October 2006 Slide 14 Set up the NDI tracking system (1) The following steps are valid for Aurora tracking system 1) Set the tracking system up following the documentation coming with the device and connect it by a serial port to the computer where the Slicer is running 2) Download IGT server and data form: http://www.na-mic.org/Wiki/index.php/IGT- Tutorials. Unzip the file and you'll find two directories: server and skull_CT. Save skull_CT for later use. http://www.na-mic.org/Wiki/index.php/IGT- Tutorials 3) Create a command prompt and change directory to “server”

15. © NIH National Center for Image-Guided Therapy, October 2006 Slide 15 Set up the NDI tracking system (2) 4 ) Install NDI ToolViewer on your computer from the CD. Power on the tracking device and run NDI ToolViewer. Find the tool ID for the 6 DOF tracking sensor. Put the value into this file “splotConfig.xml” (the toolID field) in the server directory. 5) Power off and on the tracking system. Then in the command prompt in the server directory, run this command: opentracker_spl.exe splotConfig.xml Now, move your tracking sensor and you should see the position and orientation values change in the prompt. The server is running!

16. © NIH National Center for Image-Guided Therapy, October 2006 Connect Slicer to tracking device (1) Click Locator button Click Server tab Choose Opentracker as the Active Server

17. © NIH National Center for Image-Guided Therapy, October 2006 Connect to tracking device (2) Click Locator button Click Tracking tab Click Connect button

18. © NIH National Center for Image-Guided Therapy, October 2006 Slide 18 Space registration (1)

19. © NIH National Center for Image-Guided Therapy, October 2006 Slide 19 Space registration (2) Load the CT scan of plastic skull into Slicer (File- >Import Scene->skull.xml) Adjust window and level to its best view Create a 3D model for the skull out of its CT volume. You can see 14 fiducial points on the surface Put the plastic skull inside the tracking scope of the device (500 x 500 x 500 mm) On the plastic skull, find 4 unique points. Record their coordinates in both device and Slicer spaces. Add them into Locator->Server->OpenTracker- >Registration tab. The skull model helps a lot to match points.

20. © NIH National Center for Image-Guided Therapy, October 2006 Slide 20 Space registration (3) For Pat (device) space, touch the point with the sensor and then hit button Get to save values in Slicer For Slicer space, click the point in any 2D window and the coordinates will be automatically saved in the entry field Click OK to add one pair of points. Repeat it to add 4 pairs. Then click Register to perform registration Other useful buttons: Save to write all values into a file. Load to load values from a file. Delete to remove one point pair at a time. Reset to ignore the current registration.

21. © NIH National Center for Image-Guided Therapy, October 2006 Navigation (1) Click Locator button Click Server tab Click Tracking tab Click Show Locator button Click Handle button Change the Driver from User to Locator

22. © NIH National Center for Image-Guided Therapy, October 2006 Navigation (2) Now, move the tracking sensor around the skull surface and you are navigating the “brain” in Slicer: ● The position and orientation of the sensor (the “needle”) are displayed in the 3D view. The display updates as you move the “needle.” ● The CT images of the plastic skull in 3D dimensioins also update accordingly

23. © NIH National Center for Image-Guided Therapy, October 2006 Navigation (3)

24. © NIH National Center for Image-Guided Therapy, October 2006 Slide 24 Slicer resources www.slicer.org www.na-mic.org/Wiki www.na-mic.org/Bug www.na-mic.org/Testing slicer-devel@bwh.harvard.edu slicer-users@bwh.harvard.edu